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FW: AMSI BioInfoSummer 2018 - Save the date
by Michael Charleston 17 Jul '18

17 Jul '18

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Fw: Dates for Galaxy-Australia training
by Michael Charleston 25 Jun '18

25 Jun '18

Dear Tasmanian Bioinformatics Folk, Workshops for all! There will be some free stand-alone Galaxy-based workshops run locally in the hybrid mode (like the Genome Annotation one we had last year), later in the year as below. The dates/times for these training events are now confirmed as: * Wed Aug 22 1-3pm AEST – genome assembly * Wed Sep 12 1-3pm AEST – variant detection * Tue Oct 23 1-3pm AEDT - RNA-seq * Wed Nov 14 1-3pm AEDT - metagenomics I'll be journeying to far-off Melbourne in July to a train-the-trainer workshop so I can best facilitate and answer all your questions locally. Please register your interest at any of these workshops on the Google form here<https://goo.gl/forms/o49629yFaLhaUydB2> --- NOT by return e-mail!<https://goo.gl/forms/o49629yFaLhaUydB2><https://goo.gl/forms/o49629yFaLhaUydB2> Best wishes Mike University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fwd: 2018 Winter School in Mathematical & Computational Biology (2-6 July 2018) - Student travel scholarship application CLOSE 31 MAY 2018
by Michael Charleston 01 Jun '18

01 Jun '18

Worth a look! Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics Research Group Begin forwarded message: From: Kelly Carpenter <kelly.carpenter(a)utas.edu.au<mailto:kelly.carpenter@utas.edu.au>> Subject: FW: 2018 Winter School in Mathematical & Computational Biology (2-6 July 2018) - Student travel scholarship application CLOSE 31 MAY 2018 Date: 28 May 2018 at 1:26:36 pm AEST To: Mathematics & Physics - All <SET-DL-Maths-And-Physics-All(a)utas.edu.au<mailto:SET-DL-Maths-And-Physics-All@utas.edu.au>> The 2018 Winter School in Mathematical & Computational Biology (2-6 July 2018) will be of particular interest to your students e.g. advanced undergraduate, honours, postgraduate; and postdoctoral researchers etc. If you would kindly circulate the email below within your school/faculty would be most appreciated. ** 2018 Winter School in Mathematical & Computational Biology (2-6 July 2018)** <https://protect-au.mimecast.com/s/tDkjClxwAVHXw87ncGHJWa?domain=bioinformat…>http://bioinformatics.org.au/winterschool/<https://protect-au.mimecast.com/s/tDkjClxwAVHXw87ncGHJWa?domain=bioinformat…> KEY DATES Student travel scholarships – CLOSE on 31 May 2018 Online registration - Early bird CLOSE Sunday 10 June 2018, Normal CLOSE SUNDAY 24 June 2018 The series of winter schools is designed to introduce bioinformatics, mathematical and computational biology to advanced undergraduate and postgraduate students, postdoctoral researchers and others working in the fields of biology, mathematics, statistics, computer science, information technology, complex systems analysis, and chemical and medical sciences and engineering. Themes * Next generation sequencing & bioinformatics * Data science and machine learning for bioinformatics * Bio-data analysis and visualisation * Advanced microscopy analysis and modelling Featured speakers -- John Quackenbush, Harvard University -- Melissa Little, Murdoch Children’s Research Institute -- Sean O’Donoghue, Garvan Institute of Medical Research -- Simone Linz, University of Auckland -- Cameron Bean, Artificial Intelligence for Genomics, Max Kelsen Brisbane -- Joshua Ho, Victor Chang Cardiac Research Institute Speakers at Winter School are chosen as great presenters and world leaders in their field. For the complete list of speakers and presentation titles, visit websitehttp://bioinformatics.org.au/winterschool/<https://protect-au.mimecast.com/s/tDkjClxwAVHXw87ncGHJWa?domain=bioinformat…>. Workshop & bootcamp A Genomics Virtual Laboratory training workshop (limited places) will be run during the Winter School on Wednesday 4th July. A Software Carpentry Bootcamp (9-10 July) is also being run in conjunction with the Winter School. Both events were fully subscribed in days last year, so register early to avoid disappointment. Feedback from previous Winter Schools “I would strongly encourage all biologists even without any mathematical background to attend the Winter School.” “Fantastic speakers.” “Great networking opportunities.” “It takes special talent to pull off a conference people actually enjoy attending and it was thanks to some of the more charismatic orators, that I was able to enjoy the Winter School so much.” “Gave me the confidence I need to talk to other people and bioinformaticians about the analysis of my NGS data. Thanks." Lanna Wong | Coordinator Institute for Molecular Bioscience Level 6 West | 306 Carmody Road (Building 80) | The University of Queensland | Brisbane QLD 4072 Australia T +61 7 3346 2617 |F +61 7 3346 2101 | E l.wong(a)uq.edu.au<mailto:l.wong@uq.edu.au> imb.uq.edu.au<https://protect-au.mimecast.com/s/Vp8ZCnxyDVHmZ25OcNJABf?domain=imb.uq.edu.…> | Facebook<https://protect-au.mimecast.com/s/vv0GCoVzE9HvVR4qi6E6EW?domain=facebook.com> | Twitter<https://protect-au.mimecast.com/s/_VxqCp8AG6fA0WDMuJlHnL?domain=twitter.com> | YouTube<https://protect-au.mimecast.com/s/TsIbCq7BJXtXy3W0crBqwB?domain=youtube.com> [signature]<https://protect-au.mimecast.com/s/Vp8ZCnxyDVHmZ25OcNJABf?domain=imb.uq.edu.…> This email (including any attached files) is intended solely for the addressee. It may contain private or confidential information. If you are not the intended addressee, you must take no action based on it, nor show a copy to anyone. Kindly notify the sender by reply email. Opinions and information in this email which do not relate to the official business of The University of Queensland shall be understood as neither given nor endorsed by the University. CRICOS Provider Number 00025B. University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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RE: bioinformatics-list Digest, Vol 28, Issue 1
by Sanjay Gautam 03 May '18

03 May '18

Hi bioinformatics- list, This may be useful to modelling enthusiasts. Swiss Tropical and Public Health Institute is looking for candidates for a PhD in Mathematical Modelling of Malaria. Should you be interested, please apply until 31 May 2018 on our website https://lnkd.in/dcAm7yK -----Original Message----- From: bioinformatics-list <bioinformatics-list-bounces(a)list.utas.edu.au> On Behalf Of bioinformatics-list-request(a)list.utas.edu.au Sent: Tuesday, 13 March 2018 11:55 AM To: bioinformatics-list(a)list.utas.edu.au Subject: bioinformatics-list Digest, Vol 28, Issue 1 Send bioinformatics-list mailing list submissions to bioinformatics-list(a)list.utas.edu.au To subscribe or unsubscribe via the World Wide Web, visit https://lists.utas.edu.au/mailman/listinfo/bioinformatics-list or, via email, send a message with subject or body 'help' to bioinformatics-list-request(a)list.utas.edu.au You can reach the person managing the list at bioinformatics-list-owner(a)list.utas.edu.au When replying, please edit your Subject line so it is more specific than "Re: Contents of bioinformatics-list digest..." Today's Topics: 1. Apollo workshop: November 21st (Michael Charleston) 2. New post-doctoral position available (Michael Charleston) ---------------------------------------------------------------------- Message: 1 Date: Sun, 19 Nov 2017 23:40:22 +0000 From: Michael Charleston <michael.charleston(a)utas.edu.au> To: "bioinformatics-list(a)utas.edu.au" <bioinformatics-list(a)utas.edu.au> Subject: Apollo workshop: November 21st Message-ID: <68F61762-C99F-4D58-8174-397B7C1AF9F6(a)utas.edu.au> Content-Type: text/plain; charset="us-ascii" Couple more places available locally for the workshop tomorrow: If you would like to register then the link to do so is https://genome-annotation-using-apollo-uni-tasmania.eventbrite.com.au<https://protect-au.mimecast.com/s/rNKXBofMWg8h6?domain=genome-annotation-us…> Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics in Tasmania University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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New post-doctoral position available
by Michael Charleston 13 Mar '18

13 Mar '18

http://careers.utas.edu.au/cw/en/job/492440/postdoctoral-research-fellow-in… Job no: 492440 Work type: Full time Location: Hobart Categories: Academic - Research Focus This is an opportunity to work as part of a collaborative team on an innovative project funded by an Australian Research Council Linkage Grant held jointly by the University of Tasmania, the University of Melbourne, and Monash Medical Centre. In this project we aim to analyse some healthcare systems using a variety of mathematical models with a view to better understand them, and to provide meaningful results that will enable healthcare practitioners to be better informed when making decisions. In the role you will: * Undertake high-quality research of national and international standing in the field of modelling health care systems to meet project milestones of the Australian Research Council Linkage Grant LP140100152. * Prepare scientific papers, liaise with project partners and submit manuscripts for publication. * Contribute to the preparation of progress reports to agreed stakeholders, ensuring reporting obligations to grants are met and recommendations on future directions for the research are provided. * Prepare and deliver results at relevant national and international meetings. * Make an effective and sustained contribution to the University in achieving its strategic objectives and fulfilling its operational responsibilities You will be employed on a full time, fixed term basis for 18 months. To be considered, you will have: * A PhD in mathematics or equivalent in a relevant field * Demonstrated ability to undertake high quality research in in applied probability and stochastic operations research, or a related field. * A high level of stochastic modelling skills. * Strong computational skills. * An excellent publication record in international peer-reviewed journals, relative to opportunity. Appointment to this role will be at Academic Level A, Step 6 and will have a total remuneration package of $96,121 comprising base salary of $82,155 plus 17% superannuation. For further information about this position please contact Dr Malgorzata O’Reilly, Senior Lecturer in Applied Mathematics, Malgorzata.OReilly(a)utas.edu.au / 03 6226 2405. **Please note, your application must as a minimum include your resume, a cover letter and your responses to the position/selection criteria. The position description for this role is available on the University of Tasmania website. Applications close Friday, 30 March 2018. -- Michael Charleston [/Users/mc7/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1972939931] Theoretical Phylogenetics Group Associate Professor in Bioinformatics School of Natural Sciences University of Tasmania AUSTRALIA Phone: +61 3 6226 2444 University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Apollo workshop: November 21st
by Michael Charleston 20 Nov '17

20 Nov '17

Couple more places available locally for the workshop tomorrow: If you would like to register then the link to do so is https://genome-annotation-using-apollo-uni-tasmania.eventbrite.com.au<https://protect-au.mimecast.com/s/rNKXBofMWg8h6?domain=genome-annotation-us…> Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics in Tasmania University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Apollo workshop: November 21st
by Michael Charleston 17 Nov '17

17 Nov '17

Hello all, If you would like to register then the link to do so is https://genome-annotation-using-apollo-uni-tasmania.eventbrite.com.au<https://protect-au.mimecast.com/s/rNKXBofMWg8h6?domain=genome-annotation-us…> Places are limited! Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics in Tasmania University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Apollo Training Session: EMBL-ABR
by Michael Charleston 15 Nov '17

15 Nov '17

Hi all, Remember that workshop on Genome Annotation using Apollo, that we had to cancel, but which might happen virtually? Well there's a great opportunity to join with a live webinar / tutorial presented by Monica Munoz-Torres next week, from 11 to 2pm on Tuesday November 21. There’s no charge, and no pressure, but if you’d like to come along with me and learn then please let me know. I’ll be logging in either from my computer or from a video conferencing room depending on how many people are interested. Apologies for the short notice! It kind of slipped off my radar on account of an unexpected surfeit of the usual academic mayhem. With luck and dedication we’ll also run more sessions next year, and the session will be recorded. Best wishes Mike Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics in Tasmania University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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Fwd: [Genomics_bioinformatics] Introductory workshop on Bacterial Genomics using Galaxy
by Michael Charleston 09 Nov '17

09 Nov '17

If anyone’s in/near Sydney, here’s a thing of interest! Yes, I have a new logo in my signature: it’s also to be seen on the Phylomania 2017 front page<http://www.maths.utas.edu.au/phylomania/phylomania2017.htm>, in case you meant to come but haven’t yet registered.. and there’s also the Australasian Evolution Society meeting<https://aesconference2017.wordpress.com/> on at the same time, so consider coming to both! Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444 [cid:57A171C5-21DF-4F31-B9AF-65FF92F721D1@maths.utas.edu.au] Theoretical Phylogenetics in Tasmania Begin forwarded message: From: Rosemarie Sadsad <rosemarie.sadsad(a)sydney.edu.au<mailto:rosemarie.sadsad@sydney.edu.au>> Subject: [Genomics_bioinformatics] Introductory workshop on Bacterial Genomics using Galaxy Date: 9 November 2017 at 10:15:44 AM AEDT To: "clc-users(a)mailman.sydney.edu.au<mailto:clc-users@mailman.sydney.edu.au>" <clc-users(a)mailman.sydney.edu.au<mailto:clc-users@mailman.sydney.edu.au>>, "genomics_bioinformatics(a)mailman.sydney.edu.au<mailto:genomics_bioinformatics@mailman.sydney.edu.au>" <genomics_bioinformatics(a)mailman.sydney.edu.au<mailto:genomics_bioinformatics@mailman.sydney.edu.au>>, "computing_training(a)mailman.sydney.edu.au<mailto:computing_training@mailman.sydney.edu.au>" <computing_training(a)mailman.sydney.edu.au<mailto:computing_training@mailman.sydney.edu.au>>, "artemis.users(a)mailman.sydney.edu.au<mailto:artemis.users@mailman.sydney.edu.au>" <artemis.users(a)mailman.sydney.edu.au<mailto:artemis.users@mailman.sydney.edu.au>> [cid:image001.png@01D35943.B3317480] The Sydney Informatics Hub invite you to attend a free, half day introductory workshop on Bacterial Genomics using Galaxy provided by Intersect. The Galaxy Platform is an open, web-based analysis and workflow platform designed for biologists to analyse their own data and can be used to run a variety of bioinformatics tools. Specifically, the training course will include: * How to use the Galaxy bioinformatics platform * Bacterial genome assembly and annotation * Bacterial variant calling * Galaxy workflows The RDS Omics project is an RDS-funded flagship project<https://protect-au.mimecast.com/s/aYDmBWipVgxC4?domain=rds.edu.au> to provide cloud-based data services and tools for Australian Life Science Researchers to combine, analyse and interpret genomic (DNA), transcriptomic (RNA), proteomic (proteins) and metabolomic (small molecules) data. The project is building the first Australian platform to allow 4 distinct ‘omics’ data types to be: * co-analysed and stored in one system; * managed through a common data management system; * able to have bioinformatics analysis performed on these data via a common interface * made accessible to biology researchers in Australia and internationally; * published to international repositories Please find the registration link for the Omics training below with more information about the training and the Omics project. https://www.eventbrite.com.au/e/omics-training-tickets-39467052015<https://protect-au.mimecast.com/s/2mpOBYirA64iA?domain=eventbrite.com.au> For more information about other bioinformatics, data analysis and management services and training offered by the Sydney Informatics Hub, please contact sih.info(a)sydney.edu.au<mailto:sih.info@sydney.edu.au> Please feel free to forward this on to your colleagues or research groups that may be interested. Kind regards, Rosemarie ROSEMARIE SADSAD | Informatics Services Lead Sydney Informatics Hub | Core Research Facilities Room 541, Level 5, The School of Information Technologies J12 The University of Sydney, NSW, 2006 P: +61 2 8627 6286 E: Rosemarie.Sadsad(a)sydney.edu.au<mailto:Rosemarie.Sadsad@sydney.edu.au> W: https://informatics.sydney.edu.au/<https://protect-au.mimecast.com/s/6eKrBGfGVv5FY?domain=informatics.sydney.e…> University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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AGTA annual meeting Special Day Registration and Workshop attendance for locals
by Kathryn Burdon 19 Oct '17

19 Oct '17

The Australasian Genomics Technologies Association Annual Meeting will be held in Hobart from October 29th to November 1st at the Hotel Grand Chancellor. We have assembled an array of International and Australian scientists to present and discuss genomic technologies and the biology that these technologies are uncovering. We have planned session around complex traits, population genetics, functional genomics, bioinformatics and computational biology, epigenetics and transcriptomics, comparative genomics, gene editing, medical genetics and much more! Registration for the meeting is still open and you can view the program and other meeting information here<http://agtaconference.org/>. We have two concurrent pre-conference workshops<http://agtaconference.org/pre-conference-workshops/> planned on Sunday 29th Oct: "Can genome editing fulfil its promise in the clinic and the field?" and "Technical solution to single cell problems". Both workshops include presentations from invited speakers and panel discussions in which you can participate to learn more about the utility of genome editing or the techniques available for single cell genomics. Locals are invited to attend a workshop without registering for the whole meeting. Tickets are priced at $40 each or $20 for students. We also have a special single day registration rate of $250 for locals, if you would like to attend the meeting but can only make 1 day. To take advantage of these offers, please contact Emma Harrison at Emma(a)leishman-associates.com.au<mailto:Emma@leishman-associates.com.au> directly. They are not available through the conference website. Please distribute this information through your local networks to anyone who may be interested. Hope to see you there Kathryn Burdon and Jac Charlesworth on behalf of the #AGTA17 Organising Committee [cid:image002.png@01D348D5.8CA9D290] A/Prof Kathryn Burdon | Principal Research Fellow | Cancer, Immunology & Genetics Group Menzies Institute for Medical Research | University of Tasmania Email: Kathryn.burdon(a)utas.edu.au<mailto:Kathryn.burdon@utas.edu.au> Phone: +61 3 62264288 17 Liverpool St (Private Bag 23) Hobart TAS 7000 | www.menzies.utas.edu.au<http://www.menzies.utas.edu.au/> Twitter: @kathrynpenelope [cid:image001.jpg@01CFF754.F8486000] University of Tasmania Electronic Communications Policy (December, 2014). This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

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